chr14-52275462-T-C

Variant names:

• chr14-52275462-T-C
• rs17831682
• NM_000953.3:c.*498T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000953.3(PTGDR):​c.*498T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.069 in 156,316 control chromosomes in the GnomAD database, including 496 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.069 (483 hom., cov: 32)
  • Exomes 𝑓: 0.073 (13 hom.)
• Consequence: PTGDR NM_000953.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 9 publications found

Genes affected

PTGDR (HGNC:9591): (prostaglandin D2 receptor) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein is reported to be a receptor for prostaglandin D2, which is a mediator of allergic inflammation and allergic airway inflammation in asthma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ENSG00000289424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000953.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGDR	NM_000953.3	MANE Select	c.*498T>C		3_prime_UTR	Exon 2 of 2	NP_000944.1
	PTGDR	NM_001281469.2		c.*778T>C		3_prime_UTR	Exon 3 of 3	NP_001268398.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGDR	ENST00000306051.3	TSL:1 MANE Select	c.*498T>C		3_prime_UTR	Exon 2 of 2	ENSP00000303424.2
	ENSG00000289424	ENST00000726797.1		n.300-5917A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0689 AC: 10487 AN: 152138 Hom.: 481 Cov.: 32

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0602

GnomAD4 exome AF: 0.0732 AC: 297 AN: 4060 Hom.: 13 Cov.: 0 AF XY: 0.0747 AC XY: 178 AN XY: 2384

African (AFR) AF: 0.00 AC: 0 AN: 14

American (AMR) AF: 0.0523 AC: 34 AN: 650

Ashkenazi Jewish (ASJ) AF: 0.0417 AC: 1 AN: 24

East Asian (EAS) AF: 0.0676 AC: 10 AN: 148

South Asian (SAS) AF: 0.135 AC: 44 AN: 326

European-Finnish (FIN) AF: 0.0714 AC: 3 AN: 42

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0718 AC: 197 AN: 2742

Other (OTH) AF: 0.0714 AC: 8 AN: 112

GnomAD4 genome AF: 0.0689 AC: 10494 AN: 152256 Hom.: 483 Cov.: 32 AF XY: 0.0699 AC XY: 5207 AN XY: 74440

African (AFR) AF: 0.0249 AC: 1036 AN: 41554

American (AMR) AF: 0.0601 AC: 920 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.127 AC: 655 AN: 5170

South Asian (SAS) AF: 0.156 AC: 754 AN: 4822

European-Finnish (FIN) AF: 0.0670 AC: 711 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5879 AN: 68012

Other (OTH) AF: 0.0605 AC: 128 AN: 2116

Alfa AF: 0.0818 Hom.: 820

Bravo AF: 0.0660

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17831682; hg19: chr14-52742180;